nf-core_modules/software/homer/annotatepeaks/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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def VERSION = '4.11'
process HOMER_ANNOTATEPEAKS {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::homer=4.11" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3"
} else {
container "quay.io/biocontainers/homer:4.11--pl526hc9558a2_3"
}
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input:
tuple val(meta), path(peak)
path fasta
path gtf
output:
tuple val(meta), path("*annotatePeaks.txt"), emit: txt
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
annotatePeaks.pl \\
$peak \\
$fasta \\
$options.args \\
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-gtf $gtf \\
-cpu $task.cpus \\
> ${prefix}.annotatePeaks.txt
echo $VERSION > ${software}.version.txt
"""
}